inst/doc/BiocPkgTools.R

In BiocPkgTools: Collection of simple tools for learning about Bioc Packages

## ----init, include=FALSE------------------------------------------------------
library(knitr)
opts_chunk$set(warning = FALSE, message = FALSE, cache=FALSE)

## ----style, echo = FALSE, results = 'asis'------------------------------------
BiocStyle::markdown()

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library(BiocPkgTools)
head(biocBuildReport())

## ----eval=FALSE---------------------------------------------------------------
#  problemPage()

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head(biocDownloadStats())

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bpi = biocPkgList()
colnames(bpi)

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head(bpi)

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require(dplyr)
bpi = biocPkgList()
bpi %>% 
    filter(Package=="GEOquery") %>%
    pull(importsMe) %>%
    unlist()

## ----biocExplore--------------------------------------------------------------
biocExplore()

## -----------------------------------------------------------------------------
library(BiocPkgTools)
dep_df = buildPkgDependencyDataFrame()
g = buildPkgDependencyIgraph(dep_df)
g
library(igraph)
head(V(g))
head(E(g))

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igraph_network = buildPkgDependencyIgraph(buildPkgDependencyDataFrame())

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igraph_geoquery_network = subgraphByDegree(igraph_network, "GEOquery")

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library(visNetwork)
data <- toVisNetworkData(igraph_geoquery_network)

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visNetwork(nodes = data$nodes, edges = data$edges, height = "500px")

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visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>%
    visPhysics(stabilization=FALSE)

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data$edges$color='lightblue'
data$edges[data$edges$edgetype=='Imports','color']= 'red'
data$edges[data$edges$edgetype=='Depends','color']= 'green'

visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>%
    visEdges(arrows='from') 

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ledges <- data.frame(color = c("green", "lightblue", "red"),
  label = c("Depends", "Suggests", "Imports"), arrows =c("from", "from", "from"))
visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>%
  visEdges(arrows='from') %>%
  visLegend(addEdges=ledges)

## ----biocViews----------------------------------------------------------------
library(biocViews)
data(biocViewsVocab)
biocViewsVocab
library(igraph)
g = igraph.from.graphNEL(biocViewsVocab)
library(visNetwork)
gv = toVisNetworkData(g)
visNetwork(gv$nodes, gv$edges, width="100%") %>%
    visIgraphLayout(layout = "layout_as_tree", circular=TRUE) %>%
    visNodes(size=20) %>%
    visPhysics(stabilization=FALSE)

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library(BiocPkgTools)

depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"),
                                     dependencies=c("Depends", "Imports"))
depdf

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pkgDepMetrics("BiocPkgTools", depdf)

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imp <- pkgDepImports("BiocPkgTools")
imp %>% filter(pkg == "DT")

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sessionInfo()